You might consider displaying ccgg content as a track in mouse genome
browser at
http://gbrowse.informatics.jax.org/cgi-bin/gbrowse/mouse_build_34
For example, the following track causes it to display 3 proportionally
sized red boxes in the first 3K of mouse Chr1
[MotifContent]
glyph = xyplot
graph_type = boxes
fgcolor = black
bgcolor = red
height=100
min_score=0
max_score=100
label=1
key="Motif Content"
reference=Chr1
MotifContent CCGG 1..1000 score=20
MotifContent CCGG 1001..2000 score=50
MotifContent CCGG 2001..3000 score=30
There are many ways for computing the score. I myself would begin with:
#!/usr/bin/env perl
use strict;
use Bio::SeqIO; # for reading sequence to scan
use TFBS::Word::Consensus; # for the pattern matching. cf.
http://forkhead.cgb.ki.se/TFBS/
use PDL::Basic; # if you have it installed, for the histogram binning
statistics
________________________________
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of staffa
Sent: Tuesday, February 21, 2006 11:25 AM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] Pattern Density
Good Friends,
I have an important client who wants a histogram display of the
density of "ccgg" along any chromosome of the mouse genome in 1000 bp
windows.
I'm thinking that maybe there is a bio-perl module that could
help with this.
That'd probably beat having to write something from scratch.
Any help that you give would be greatly appreciated.
I am more concerned about the reading and analysis of the
sequence than actual plotting of the histogram, but anything you can
offer will be appreciated.
Thank you.
Nick Staffa
Telephone: 919-316-4569 (NIEHS: 6-4569)
Scientific Computing Support Group
NIEHS Information Technology Support Services Contract
(Science Task Monitor: Jack L. Field( field1 at niehs.nih.gov )
National Institute of Environmental Health Sciences
National Institutes of Health
Research Triangle Park, North Carolina